WHAT IF Check report

This file was created 2011-12-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1anp.ent

Administrative problems that can generate validation failures

Error: Calpha only residues

WHAT IF has detected residues that contain just an alpha carbon atom and nothing else. The many missing atoms make it hard for WHAT IF to properly validate the environment of these residues. Consequently, you are suggested to be careful when using the WHAT CHECK report.

   1 SER   (   1-)  A  1
   2 LEU   (   2-)  A  1
   3 ASP   (   3-)  A  1
   4 ARG   (   4-)  A  1
   5 SER   (   5-)  A  1
   6 SER   (   6-)  A  1
   7 CYS   (   7-)  A  1
   8 PHE   (   8-)  A  1
   9 THR   (   9-)  A  1
  10 GLY   (  10-)  A  1
  11 SER   (  11-)  A  1
  12 LEU   (  12-)  A  1
  13 ASP   (  13-)  A  1
  14 SER   (  14-)  A  1
  15 ILE   (  15-)  A  1
  16 ARG   (  16-)  A  1
  17 ALA   (  17-)  A  1
  18 GLN   (  18-)  A  1
  19 SER   (  19-)  A  1
  20 GLY   (  20-)  A  1
  21 LEU   (  21-)  A  1
  22 GLY   (  22-)  A  1
  23 CYS   (  23-)  A  1
  24 ASN   (  24-)  A  1
  25 SER   (  25-)  A  1
And so on for a total of 308 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 SER   (   1-)  A  1   N
   1 SER   (   1-)  A  1   C
   1 SER   (   1-)  A  1   O
   1 SER   (   1-)  A  1   CB
   1 SER   (   1-)  A  1   OG
   2 LEU   (   2-)  A  1   N
   2 LEU   (   2-)  A  1   C
   2 LEU   (   2-)  A  1   O
   2 LEU   (   2-)  A  1   CB
   2 LEU   (   2-)  A  1   CG
   2 LEU   (   2-)  A  1   CD1
   2 LEU   (   2-)  A  1   CD2
   3 ASP   (   3-)  A  1   N
   3 ASP   (   3-)  A  1   C
   3 ASP   (   3-)  A  1   O
   3 ASP   (   3-)  A  1   CB
   3 ASP   (   3-)  A  1   CG
   3 ASP   (   3-)  A  1   OD1
   3 ASP   (   3-)  A  1   OD2
   4 ARG   (   4-)  A  1   N
   4 ARG   (   4-)  A  1   C
   4 ARG   (   4-)  A  1   O
   4 ARG   (   4-)  A  1   CB
   4 ARG   (   4-)  A  1   CG
   4 ARG   (   4-)  A  1   CD
And so on for a total of 2002 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 SER   (   1-)  A  1   Zero
   2 LEU   (   2-)  A  1   Zero
   3 ASP   (   3-)  A  1   Zero
   4 ARG   (   4-)  A  1   Zero
   5 SER   (   5-)  A  1   Zero
   6 SER   (   6-)  A  1   Zero
   7 CYS   (   7-)  A  1   Zero
   8 PHE   (   8-)  A  1   Zero
   9 THR   (   9-)  A  1   Zero
  10 GLY   (  10-)  A  1   Zero
  11 SER   (  11-)  A  1   Zero
  12 LEU   (  12-)  A  1   Zero
  13 ASP   (  13-)  A  1   Zero
  14 SER   (  14-)  A  1   Zero
  15 ILE   (  15-)  A  1   Zero
  16 ARG   (  16-)  A  1   Zero
  17 ALA   (  17-)  A  1   Zero
  18 GLN   (  18-)  A  1   Zero
  19 SER   (  19-)  A  1   Zero
  20 GLY   (  20-)  A  1   Zero
  21 LEU   (  21-)  A  1   Zero
  22 GLY   (  22-)  A  1   Zero
  23 CYS   (  23-)  A  1   Zero
  24 ASN   (  24-)  A  1   Zero
  25 SER   (  25-)  A  1   Zero
And so on for a total of 308 lines.

Torsion-related checks

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   2 LEU   (   2-)  A  1 Impossible phi
   3 ASP   (   3-)  A  1 Impossible phi
   4 ARG   (   4-)  A  1 Impossible phi
   5 SER   (   5-)  A  1 Impossible phi
   6 SER   (   6-)  A  1 Impossible phi
   7 CYS   (   7-)  A  1 Impossible phi
   8 PHE   (   8-)  A  1 Impossible phi
   9 THR   (   9-)  A  1 Impossible phi
  10 GLY   (  10-)  A  1 Impossible phi
  11 SER   (  11-)  A  1 Impossible phi
  12 LEU   (  12-)  A  1 Impossible phi
  13 ASP   (  13-)  A  1 Impossible phi
  14 SER   (  14-)  A  1 Impossible phi
  15 ILE   (  15-)  A  1 Impossible phi
  16 ARG   (  16-)  A  1 Impossible phi
  17 ALA   (  17-)  A  1 Impossible phi
  18 GLN   (  18-)  A  1 Impossible phi
  19 SER   (  19-)  A  1 Impossible phi
  20 GLY   (  20-)  A  1 Impossible phi
  21 LEU   (  21-)  A  1 Impossible phi
  22 GLY   (  22-)  A  1 Impossible phi
  23 CYS   (  23-)  A  1 Impossible phi
  24 ASN   (  24-)  A  1 Impossible phi
  25 SER   (  25-)  A  1 Impossible phi
  26 PHE   (  26-)  A  1 Impossible phi
And so on for a total of 286 lines.

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  11 SER   (  11-)  A  1     0
  12 LEU   (  12-)  A  1     0
  27 ARG   (  27-)  A  1     0
  28 TYR   (  28-)  A  1     0
  29 SER   (   1-)  A  2     0
  30 LEU   (   2-)  A  2     0
  53 SER   (  25-)  A  2     0
  54 PHE   (  26-)  A  2     0
  55 ARG   (  27-)  A  2     0
  56 TYR   (  28-)  A  2     0
  57 SER   (   1-)  A  3     0
  58 LEU   (   2-)  A  3     0
  80 ASN   (  24-)  A  3     0
  83 ARG   (  27-)  A  3     0
  84 TYR   (  28-)  A  3     0
  85 SER   (   1-)  A  4     0
  86 LEU   (   2-)  A  4     0
  87 ASP   (   3-)  A  4     0
  97 ASP   (  13-)  A  4     0
 103 SER   (  19-)  A  4     0
 108 ASN   (  24-)  A  4     0
 109 SER   (  25-)  A  4     0
 111 ARG   (  27-)  A  4     0
 112 TYR   (  28-)  A  4     0
 113 SER   (   1-)  A  5     0
And so on for a total of 107 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

  33 SER   (   5-)  A  2  4.99   33
   5 SER   (   5-)  A  1  4.31   16
 146 SER   (   6-)  A  6  2.44   19

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 1

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 2

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 3

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 4

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 5

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 6

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 7

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 8

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 9

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 10

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A; Model number 11

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 116 ARG   (   4-)  A  5  -3.96
 172 ARG   (   4-)  A  7  -3.96
 200 ARG   (   4-)  A  8  -3.96
  18 GLN   (  18-)  A  1  -3.70
  46 GLN   (  18-)  A  2  -3.70
  74 GLN   (  18-)  A  3  -3.70
 130 GLN   (  18-)  A  5  -3.70
 158 GLN   (  18-)  A  6  -3.70
 186 GLN   (  18-)  A  7  -3.70
 214 GLN   (  18-)  A  8  -3.70
 270 GLN   (  18-)  A 10  -3.70
 298 GLN   (  18-)  A 11  -3.70
 241 ALA   (  17-)  A  9  -3.59
 301 LEU   (  21-)  A 11  -3.49
   8 PHE   (   8-)  A  1  -3.34
  92 PHE   (   8-)  A  4  -3.34
 120 PHE   (   8-)  A  5  -3.34
 204 PHE   (   8-)  A  8  -3.34
 232 PHE   (   8-)  A  9  -3.34
 260 PHE   (   8-)  A 10  -3.34
 196 TYR   (  28-)  A  7  -3.26
  45 ALA   (  17-)  A  2  -3.14
 101 ALA   (  17-)  A  4  -3.14
 129 ALA   (  17-)  A  5  -3.14
 102 GLN   (  18-)  A  4  -3.09
And so on for a total of 83 lines.

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

  14 SER   (  14-)  A  1  -   18 GLN   (  18-)  A  1     -2.56
  25 SER   (  25-)  A  1  -   28 TYR   (  28-)  A  1     -2.24
  31 ASP   (   3-)  A  2  -   36 PHE   (   8-)  A  2     -2.11
  42 SER   (  14-)  A  2  -   46 GLN   (  18-)  A  2     -2.71
  53 SER   (  25-)  A  2  -   56 TYR   (  28-)  A  2     -2.48
  69 ASP   (  13-)  A  3  -   75 SER   (  19-)  A  3     -2.23
  80 ASN   (  24-)  A  3  -   84 TYR   (  28-)  A  3     -2.31
  87 ASP   (   3-)  A  4  -   92 PHE   (   8-)  A  4     -2.13
  97 ASP   (  13-)  A  4  -  102 GLN   (  18-)  A  4     -2.39
 109 SER   (  25-)  A  4  -  112 TYR   (  28-)  A  4     -2.36
 117 SER   (   5-)  A  5  -  120 PHE   (   8-)  A  5     -2.21
 123 SER   (  11-)  A  5  -  130 GLN   (  18-)  A  5     -2.47
 137 SER   (  25-)  A  5  -  140 TYR   (  28-)  A  5     -2.08
 143 ASP   (   3-)  A  6  -  148 PHE   (   8-)  A  6     -2.04
 153 ASP   (  13-)  A  6  -  158 GLN   (  18-)  A  6     -2.31
 165 SER   (  25-)  A  6  -  168 TYR   (  28-)  A  6     -2.24
 173 SER   (   5-)  A  7  -  176 PHE   (   8-)  A  7     -2.08
 181 ASP   (  13-)  A  7  -  186 GLN   (  18-)  A  7     -2.28
 193 SER   (  25-)  A  7  -  196 TYR   (  28-)  A  7     -2.31
 210 SER   (  14-)  A  8  -  214 GLN   (  18-)  A  8     -2.63
 220 ASN   (  24-)  A  8  -  224 TYR   (  28-)  A  8     -2.00
 229 SER   (   5-)  A  9  -  232 PHE   (   8-)  A  9     -2.21
 238 SER   (  14-)  A  9  -  242 GLN   (  18-)  A  9     -2.75
 249 SER   (  25-)  A  9  -  252 TYR   (  28-)  A  9     -2.08
 257 SER   (   5-)  A 10  -  260 PHE   (   8-)  A 10     -2.20
 265 ASP   (  13-)  A 10  -  270 GLN   (  18-)  A 10     -2.31
 277 SER   (  25-)  A 10  -  280 TYR   (  28-)  A 10     -2.35
 294 SER   (  14-)  A 11  -  298 GLN   (  18-)  A 11     -2.56
 305 SER   (  25-)  A 11  -  308 TYR   (  28-)  A 11     -2.08

Note: Per-model averages for NQA

The table below gives the per-model NQA averages and Z-scores. These are the numbers for all contacts.

Model 1 : -2.139; -11.848
Model 2 : -2.191; -12.130
Model 3 : -2.144; -11.874
Model 4 : -2.137; -11.838
Model 5 : -2.209; -12.229
Model 6 : -2.086; -11.554
Model 7 : -2.145; -11.880
Model 8 : -2.152; -11.919
Model 9 : -2.091; -11.580
Model 10 : -2.156; -11.939
Model 11 : -2.057; -11.394

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Water, ion, and hydrogenbond related checks

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  2nd generation packing quality : -11.394 (bad)
  Backbone conformation          :   0.586

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.000 (tight)
  Side chain planarity           :   0.000 (tight)
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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      Errors in protein structures
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
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      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
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      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
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      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.